Kepler was indeed a Lutheran (and not a Catholic as I incorrectly stated earlier), a Lutheran who did almost all of his important work at the court of the Holy Roman Emperor, the most Catholic of Catholic courts in Europe outside of the Vatican. He did his work in Prague, a Catholic imperial capital. He was protected by the Catholic princes and did he work for them.
You say he worked far away from papal authority.
No. He worked at the court of the Catholic Emperors of Germany.
"the most Catholic of Catholic courts" ? You must be joking.
Does 'Defenestration(s) of Prague' ring any bells?
Bohemian Jan Hus was the first of the Protestant break-aways. After he was burned at the stake for heresy, his followers (including many knights and nobles of Bohemia and Moravia) rose up in revolt. King Wenceslaus (who was sympathetic to Jan Hus) died and his brother Sigismund attempted to take the throne. But the Hussite forces ejected Sigismund and the Roman clergy along with him.
After eighteen years of war and mostly Hussites victories, the treaty of Jihlava allowed Holy Roman Emperor Sigismund to take the throne, however the lands of the Roman Catholic church were forfeit, and the churchs of Bohemia could follow the Utraquist (Hussite) creed.
Following Sigismund, Bohemia was ruled by a succession of Hapsburg (Austria) kings. One of whom, George of Podebrady, was the first King in Europe to renounce the Catholic faith and accept the early Protestant religion of Jan Hus.
After Bohemia and Hungary were recaptured from the Ottoman empire, Habsburgs were back on the throne. But they still held to the treaty of Jihlava, despite threats from the Vatican. And in Kepler's time at Prague, Emperor Rudolf II even expanded it with royal charter called the Majestät (or "Majestic Letter") in 1609 that guaranteed religious freedom to the nobles and cities.